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Spencer is correct. The boat on the flight deck is what housed the remote firing system that initiated the firing train. We attached nonel ( no electric firing cord ) to the initiation point then ran the nonel through the flight deck to detonating cord which branched to various areas of the ship to the main charges.
Tom is correct that the boat isn't actually strapped down. It is sitting on a frame.
When the ship sank, the boat was left floating on the surface.
How would I know you may ask? I was one of the Navy Explosive Ordnance Disposal technicians that set the charges to sink the USS Oriskany.
I wrote a small article about my experience sinking the Oriskany. It can be viewed here